Sequencing of the interferon regulatory factor 6 (IRF6) gene and correlation to its phenotypes in familial non-syndromic cleft lip and palate in North Indian population
The incidence of orofacial clefting varies depending upon geographical location, ethnicity, sex and even socioeconomic status. The study aimed to test the contribution of interferon regulatory factor 6 (IRF6) gene allelic variation to the incidence of non-syndromic cleft lip and/or cleft palate (CL/P) from the population of North India.
Patients from 12 North Indian families with non-syndromic cleft lip with or without cleft palate (NSCL/P) with at least two members affected were clinically evaluated and tested. DNA was extracted from the blood, and three exonic part of the IRF6 gene (exons 2, 5 and 7) were amplified by PCR. Direct sequencing was performed by PCR product, and sequencing results were compared with the reference DNA sequence of the IRF6 gene.
Three SNPs (rs861019, rs2013162 and rs2235372) in 4 out of 12 families were observed. SNP rs861019 was detected in family no. 4 (F4) around exon 2, SNP 2013162 was detected in family no. 10 (F10) and SNP 2235372 was detected in family nos. 5 and 9 (F5 and F9).
This study demonstrates that the three SNPs within the IRF6 gene are associated with NSCL/P, suggesting IRF6 gene sequence variability and variation in this gene, providing first genetic clue to the NSCL/P phenotype in North Indian families. This is our initial step to demonstrate the involvement of the IRF6 gene in NSCL/P patients in North India. Further extensive study and statistical analysis are needed to validate our result.
Level of Evidence: Level IV, diagnostic study.
KeywordsNon-syndromic cleft lip with or without cleft palate IRF6 gene SNP (rs861019 rs2013162 rs2235372) Cleft lip and palate
- 10.Stanier P, Moore GE (2004) Genetics of cleft lip and palate: syndromic genes contribute to the incidence of non-syndromic clefts. Hum Mol Genet 1:13Google Scholar
- 18.NCBI (2011) Single nucleotide polymorphism, NCBI database (dbSNP), build 126. http://www.ncbi.nlm.nih.gov/pro-jects/SNP/index.html. Accessed 12 Jan 2011
- 19.Ensembl (2011) Ensembl genome browser. http://www.ensembl.org/index.htm. Accessed 12 Jan 2011
- 20.EMBL-EBI (2011) Multiple sequence alignment programs for DNA or proteins. http://www.ebi.ac.uk/Tools/msa/clustalw2/. Accessed 12 Jan 2011
- 25.Scapoli L, Palmieri A, Martinelli M, Pezzetti F, Carinci P, Tognon M et al (2005) Strong evidence of linkage disequilibrium between polymorphisms at the IRF6 locus and nonsyndromic cleft lip with or without cleft palate, in an Italian population. Am J Hum Genet 76:180–183PubMedCentralPubMedCrossRefGoogle Scholar
- 27.Morkūnienė A, Steponavičiūtė D, Kasnauskienė J, Kučinskas V (2006) Nucleotide sequence changes in the MSX1 and IRF6 genes in Lithuanian patients with nonsyndromic orofacial clefting. Acta Med Lituanica 13(4):219–225Google Scholar